Bourret_env_and_pca_factors

Environmental data used in the principal component analysis and 10 pca factors values obtained and used in the redundancy analysis

A ddRAD Based Linkage Map of the Cultivated Strawberry, <i>Fragaria xananassa</i>

<div><p>The cultivated strawberry (<i>Fragaria</i> ×<i>ananassa</i> Duch.) is an allo-octoploid considered difficult to disentangle genetically due to its four relatively similar sub-genomic chromosome sets. This has been alleviated by the recent release of the strawberry IStraw90 whole genome genotyping array. However, array resolution relies on the genotypes used in the array construction and may be of limited general use. SNP detection based on reduced genomic sequencing approaches has the potential of providing better coverage in cases where the studied genotypes are only distantly related from the SNP array’s construction foundation. Here we have used double digest restriction-associated DNA sequencing (ddRAD) to identify SNPs in a 145 seedling F₁ hybrid population raised from the cross between the cultivars Sonata (♀) and Babette (♂). A linkage map containing 907 markers which spanned 1,581.5 cM across 31 linkage groups representing the 28 chromosomes of the species. Comparing the physical span of the SNP markers with the <i>F</i>. <i>vesca</i> genome sequence, the linkage groups resolved covered 79% of the estimated 830 Mb of the <i>F</i>. ×<i>ananassa</i> genome. Here, we have developed the first linkage map for <i>F</i>. ×<i>ananassa</i> using ddRAD and show that this technique and other related techniques are useful tools for linkage map development and downstream genetic studies in the octoploid strawberry.</p></div

A SNP-based linkage map of a <i>F</i>. <i>×ananassa</i> mapping population derived from the cross ‘Sonata’ <i>×</i> ‘Babette’.

<p>Map distances are given in centi-Morgans (cM), marker colours indicate: Red–markers segregating in the ‘Sonata’ genetic background only; Blue–markers segregating in the ‘Babette’ genetic background only; Black–markers segregating in both genetic backgrounds (1:1:1:1 and 1:2:1 segregations are indicated with bold and underscore respectively).</p

Marey Map plots of SNPs mapped to positions on the 28 <i>F</i>. <i>×ananassa</i> chromosomes vs. their physical positions on the v2.0 <i>F</i>. <i>vesca</i> (<i>Fvb</i>) pseudomolecules.

<p>Linkage sub-group fragments for groups LG5D, LG6C and LG7B have been joined with an artificial gap of 10 cM between fragments to facilitate data visualization.</p

Summary statistics for the 31 linkage group fragments that comprise the S×B linkage map, including the total number of markers mapped per linkage group, the numbers and proportions of the different segregation classes, the proportion of markers heterozygous in each parental genome, linkage group lengths and the physical distances associated with each group on the v2.0 <i>F</i>. <i>vesca</i> genome sequence.

<p>^*LG physical start: Position of the first mapped marker on the <i>Fvb</i> genome sequence. LG physical end: Position of the last mapped marker on the <i>Fvb</i> sequence. Total physical span: The distance between these markers.</p><p>Summary statistics for the 31 linkage group fragments that comprise the S×B linkage map, including the total number of markers mapped per linkage group, the numbers and proportions of the different segregation classes, the proportion of markers heterozygous in each parental genome, linkage group lengths and the physical distances associated with each group on the v2.0 <i>F</i>. <i>vesca</i> genome sequence.</p

TOB VS STW populations_text

raw dataset with 3980 SNP genotypes for two wild Atlantic salmon populations from the Tobique River and the Stewiacke River in the Bay of Fundy, Canada

Bayescan_Fdist2.tar.gz

This archive contains files used by Pritchard et al. (2016) for Fst outlier analyses: Index.txt - index of SNPs. Bayescan*.in - Bayescan input files, SNPs in index order. Fdist*.in -Fdist2 input files, SNPs in index order. datacal.c; fdist2.c; Original_README_fdist2 - Fdist2 source code & information. R_code_for_analysing_Fdist2_output.txt - modified R code from Lotterhos & Whitlock (2014). See README file in archive for further information

Map of northern Europe indicating the study populations: anadromous Atlantic Ocean, <i>G. salaris</i> susceptible (red); anadromous Baltic, moderately resistant (blue); landlocked, resistant to the parasite (green).

<p>Map of northern Europe indicating the study populations: anadromous Atlantic Ocean, <i>G. salaris</i> susceptible (red); anadromous Baltic, moderately resistant (blue); landlocked, resistant to the parasite (green).</p

Example of the results of a candidate region analysis (chromosome 23, design 1): search for regions of reduced genetic diversity in landlocked populations.

<p>A. One of the three populations, LL_PYA. SNP <i>GD</i> values (black dots), kernel-smoothed distribution of GD (black line) along the chromosome and the 99% confidence interval (area within grey lines) are shown. Distributions of logarithmically scaled p-values for elevated (blue) and reduced (red) GD statistic are plotted below. B. Smoothed <i>GD</i> curves for all three populations. Horizontal bars indicate regions of significant (p≤0.01) reduction of GD. Vertical grey shading represents region which is significant in all three populations and which has been considered further as one of a candidate regions under selection, detected by design 1.</p

Final overlap of results based on all applied designs: genome-wide evidence of directional selection.

<p>Vertical coloured shadings (green) show genomic regions, where two or three regions detected by kernel-smoothing-based designs overlap. “Parasite” (red) and “salinity” (blue) single outlier SNPs from design 4 are plotted as smaller vertical lines. Chromosome numbers are given, chromosomes bearing regions exclusively containing “parasite outliers” are marked with red font colour, and “salinity outliers” - with blue.</p